INFO : Successfully started log file 'model.loop.log' ________________________________________________________________________________ Nova Protein structure prediction by fragment assembly (Ver. 0.6.6) ________________________________________________________________________________ INFO : Printing configuration for program 'nova' INFO : Configuration file '/bmm/www/servers/phyre2/bin/loop_local.config' ________________________________________________________________________________ [Query Input] FASTA_FILE = /bmm/www/servers/phyre2/public_html/phyre2_output/d378a2000e860cdb/input.fasta PSSM_FILE = /bmm/www/servers/phyre2/public_html/phyre2_output/d378a2000e860cdb/assembler.pssm MODEL_START_LIST = model_start.list BUILD_INITIAL_REFERENCE = 0 BUILD_UP_MAX_MODELS = 1 ________________________________________________________________________________ [Energy Functions] PP_STUB = /bmm/www/servers/phyre2/bin/assembler_data/default.pp SP_STUB = /bmm/www/servers/phyre2/bin/assembler_data/default.sp BBDEP_LIBRARY_THRESHOLD = 0.9 RADIUS_OF_GYRATION_THRESHOLD = 2 RADIUS_OF_GYRATION_ABSOLUTE = 0 CBCB_CONTACT_DIST = 7.5 CONTACT_GAP = 5 MAXSUB_DIST = 6 MAXSUB_ITER = 1 RMSD_DIST = 6 HBOND_SEPARATION = 5 RESIDUE_PROB_CUT_OFF = 0.2 PP_RESIDUE_PROB_CUT_OFF = 0.4 MAX_CALIBRATE_ENERGY = 500 CUTOFF_PHI_PSI = 0.001 TORSION_BILINEAR = 1 LJ_SWITCH_RATIO = 0.7 ENERGY_SET_MODE = 0 NUMBER_OF_ENERGY_SETS = 1 ________________________________________________________________________________ [Energy Set 1] T_LIMIT = 0 WEIGHT_PAIR_POTENTIAL = 0.215 WEIGHT_SOLVATION_POTENTIAL = 1 WEIGHT_STERIC_ENERGY = 5.03 WEIGHT_RADIUS_OF_GYRATION = 2.83 WEIGHT_TORSION_ENERGY = 1.14 WEIGHT_HBONDS_ORIENT = 5.27 STERIC_CLASH = 1 PAIR_SEPARATION_MIN = 3 SS_METHOD = 0 ENERGY_SCALE_FACTOR = 0 ________________________________________________________________________________ PROB_REFINE_HELIX = 1 PROB_REFINE_SHEET = 1 PROB_REFINE_COIL = 1 ________________________________________________________________________________ PROB_SHEAR_STRAND_C = 0 PROB_PHI_PSI_TWIST_C = 0 PROB_PHI_PSI_TILT_C = 0 PROB_TEMPLATE_SPLICE_C = 0 PROB_FRAG_9_C = 0 PROB_FRAG_3_C = 1 PROB_GUNN_COST_9_C = 0 PROB_GUNN_COST_3_C = 0 PROB_STABILISE_TWIST_C = 0 PROB_STABILISE_TILT_C = 0 PROB_STABILISE_TEMPLATE_C = 0 PROB_STABILISE_FRAG_9_C = 0 PROB_STABILISE_FRAG_3_C = 0 PROB_STABILISE_GUNN_9_C = 0 PROB_STABILISE_GUNN_3_C = 0 ________________________________________________________________________________ FULL_ATOM_MODEL = 0 ________________________________________________________________________________ [Model Building] MAX_MODELS = 1000 MAX_BUILD_ITERATIONS = 100 MAX_JOIN_ITERATIONS = 5 MAX_JOIN_REFINE_ITERATIONS = 5 MAX_REFINE_ITERATIONS = 5 MAX_SPLICE_ITERATIONS = 5 SHEAR_STRAND_DISTANCE = 3.8 PHI_PSI_TWIST_LENGTH = 3 PHI_PSI_TWIST_RANGE = 5 PHI_PSI_TILT_LENGTH = 5 PHI_PSI_TILT_RANGE = 15 STABILISE_SIZE = 5 STABILISE_RESTRICT = 1 STABILISE_ITERATIONS = 3 STABILISE_BREAK_THRESHOLD = 1 STABILISE_HELIX = 0 STABILISE_STRAND = 1 STABILISE_MAX_ANGLE_UPDATE = 15 STABILISE_UPDATE_FRACTION = 1 SHEAR_LOOP_SIZE = 8 SHEAR_LOOP_COIL_SIZE = 5 SHEAR_MAX_CCD_ITERATIONS = 300 SHEAR_CCD_THRESHOLD = 0.3 SHEAR_CCD_NC_THRESHOLD = 0.1 SHEAR_CCD_RESTRICT = 0 SHEAR_MAX_ANGLE_UPDATE = 15 SHEAR_MAX_UPDATE_FRACTION = 1 REPACK_FREQUENCY = 25 REPACK_RANDOM = 2 REPACK_THRESHOLD = 0.7 GUNN_COST_UPPER = 0.03 GUNN_COST_LOWER = 11.4701 MAX_MSD_DEVIATION = 16 RESEED_RESTRICTION_INTERVAL = 0 RANDOM_LIST_L = 0 RANDOM_LIST_9 = 0 RANDOM_LIST_3 = 0 RANDOM_LIST_TEMPLATE = 0 RANDOM_BUILD = 0 ________________________________________________________________________________ [Simulated Annealing] T_START_TEMP = 10 T_END_TEMP = 0 CALIBRATION_SEED = 0 T_CALIBRATION_FACTOR = 10 ENERGY_CALIBRATION_FACTOR = 4 MAX_CALIBRATE_START = 500 T_CALIBRATION_FACTOR = 10 T_REDUCE_FACTOR_EXP = 0.5 T_REDUCE_FACTOR_STEPS = 50 RATIO_EXP_TO_LINEAR_SWITCH = 1 MIN_TEMP_THRESHOLD = 0 MAX_TEMP_ITER = 1000 MAX_TEMP_REFINE = 100 MAX_STOP_ITER = 30000 MAX_STOP_REFINE = 2000 DELTA_ROLL_SIZE = 0 DELTA_STOP_THRESHOLD = 0 MAX_QUENCH = 5000 NO_TEMPLATE_RATIO = 0.2 ________________________________________________________________________________ [Loop Modelling] MODEL_LOOPS = 1 LOOP_DATABASE = /data/data/blast/loopdb MIN_LOOP_SIZE = 2 MAX_LOOP_SIZE = 15 POSITIONAL_GAPS = 1 TRIM_BACK = 1 TRIM_BACK_STERIC_CHECKS = 0 MAX_TRIM_RES = 6 MAX_TRIM_EDGE = 6 TRIM_BACK_GOODNESS = 1 SIZE_TRIM_BACK_AV = 0 MAX_SELECT_LOOPS = 500 TOLERANCE = 0.75 RMSD_WEIGHT = 80.5 RMSD_BENCHMARK = 0 FIT_ON_TRIANGLE = 0 CHECK_STERIC_CLASH = 1 CHECK_STERIC_ENERGY = 0 STERIC_ENERGY_THRESHOLD = 0.5 ABINITIO_LOOPS = 0 ABINITIO_ENDS = 0 ABINITIO_TRIM_COUNT = 0 MAX_LOOP_MODELS = 1000 CCD_LOOP_CLOSURE_TOLERANCE = 6 CCD_FAILURE_TOLERANCE = 0 LOOP_SELECTION_TOLERANCE = 9 MAX_CCD_LOOPS = 20 CCD_DIRECTION = 1 CCD_CLOSURE_RMSD = 0.08 CCD_CLOSURE_NC_DEVIATION = 0.1 CCD_MAX_ITER = 5000 CCD_RESTRICT = 1 CCD_MAX_ANGLE_UPDATE = 15 CCD_MAX_UPDATE_FRACTION = 1 MAX_COMBINE_LOOPS = 10 START_T = 2 STEPS_PER_LOOP = 100 REPLACE_TRIMMED = 1 KNOT_FIND = 1 ________________________________________________________________________________ [Logging] LOG_LEVEL = 1 LOG_TIME = 0 LOG_FILE = 0 LOG_FILE_NAME = model.loop.log FOLDING_PATH = 0 OUTPUT_DIR = loop USE_COMPRESSION = 0 FIT_ON_PREVIOUS = 0 USAGE_FILE = nova.model_usage MODEL_START_NO = 1 MODEL_END_NO = 0 OUTPUT_FREQUENCY = 100 UNWEIGHTED_OUTPUT = 0 SPLICE_INFO = 1 SPLICE_FILE = nova.splice_info FRAGVAR_INFO = 0 BAD_FRAG_DIR = nova_bad REFINE_RRG_LIMIT = 0 STOP_FILE = assembler.stop OUTPUT_LOOPS = 0 ________________________________________________________________________________ [Benchmark] BACKBONE_RMSD = 0 OUTPUT_RMSD = 0 OUTPUT_MAXSUB = 0 REFINE_STATS_FREQUENCY = 0 REFINE_STATS_MAX = 20 REFINE_TIME_FREQUENCY = 0 REFINE_TIME_MAX = 5000 MAXSUB_DIST = 6 MAXSUB_ITER = 0 ________________________________________________________________________________ INFO : Reading FASTA sequence file INFO : Reading query PSSM file INFO : Reading Pair-potential file INFO : Reading Solvation-potential file INFO : Reading PDB list file 'model_start.list' INFO : Successfully read 0 PDBs INFO : Successfully read 1 / 1 PDBs from list file 'model_start.list' INFO : Initialising build models routine INFO : Energy Set 1 - C cumul prob_shear_strand = 0.000000 INFO : Energy Set 1 - C cumul prob_phi_psi_twist = 0.000000 INFO : Energy Set 1 - C cumul prob_phi_psi_tilt = 0.000000 INFO : Energy Set 1 - C cumul prob_template_splice = 0.000000 INFO : Energy Set 1 - C cumul prob_frag_9 = 0.000000 INFO : Energy Set 1 - C cumul prob_frag_3 = 1.000000 INFO : Energy Set 1 - C cumul prob_gunn_cost_9 = 1.000000 INFO : Energy Set 1 - C cumul prob_gunn_cost_3 = 1.000000 ________________________________________________________________________________ INFO : Entering build loops routine ________________________________________________________________________________ INFO : Processing starting model 1 - d2fbha1.20.pdb ________________________________________________________________________________ INFO : Performing trim back ________________________________________________________________________________ INFO : Modelling loops WARN : Model missing 236 N-terminal residues WARN : Model missing 8 C-terminal residues ________________________________________________________________________________ INFO : Assembling final models for 0 gaps => 1 combinations INFO : Removing single loop lists INFO : Assembled 1 / 1 combinations ________________________________________________________________________________ INFO : Ranking final models by energy INFO : Outputting models to dir 'loop/model.1' INFO : model.1.pdb : Energy = -37.074 (T = 0) : I = 0 : R = 0 : RoG = 25.702 : PP = -4.310 : SP = -0.347 : SE = 0.382 : HO = -55.486 : TE = -3.015889 ________________________________________________________________________________ INFO : Model building complete 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